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What the reconciliation must establish
A refund-ready export file should let another person trace one transaction through three records without guessing:
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- the export invoice and sales register;
- the outward-supply data filed in GSTR-1; and
- the customs record, such as a shipping bill or bill of export.
You also need evidence that the relevant return obligations and export reporting conditions have been met. The exact checks differ according to whether you exported goods or services and whether you paid IGST at export or exported under a Letter of Undertaking (LUT).
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Do not treat a portal-generated refund status as a substitute for this comparison. A field can be populated electronically and still be wrong in the accounting records, the customs document or the selected refund route.
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Choose the refund route before checking the data
Exports are generally zero-rated inter-State supplies. GST Portal guidance describes two broad routes, and the records you reconcile depend on the route selected.
| Route | Was IGST paid on export? | What is claimed? | Main mechanism identified in the guidance | Core reconciliation focus |
|---|---|---|---|---|
| Export of goods with payment of IGST | Yes | Refund of IGST paid on the exported goods | Rule 96 of the CGST Rules, with shipping-bill data transmitted through the customs process | GSTR-1 Table 6A, shipping bill or bill of export, export-manifest/report condition, and valid GSTR-3B |
| Export without payment of IGST | No | Refund of eligible unutilized input tax credit | LUT route; GST Portal identifies Form GST RFD-11 for the LUT | Invoice and GSTR-1 reporting, LUT status, eligible ITC and the evidence required for the applicable refund application |
| Export of services with payment of IGST | Yes | Refund of IGST paid on the service export | Rule 96 refers export-of-services applications to RFD-01 under Rule 89 | Service-export eligibility and the Rule 89/RFD-01 evidence set, rather than a goods shipping-bill match |
| Export of services without payment of IGST | No | Refund of eligible unutilized ITC | LUT and the relevant Rule 89/RFD-01 process | Service-export documents, LUT and eligible credit records |
This table is a route-selection framework, not an eligibility opinion. Confirm the facts of the transaction and the current portal instructions before filing. A goods-export Rule 96 workflow should not be applied mechanically to services.
Assemble the records and create one invoice-level population
Start with the export sales register
Export the complete invoice list for the period from your accounting or invoicing system. Give each row a stable internal identifier and retain at least:
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- tax invoice number and date;
- customer and destination details used by your internal controls;
- total invoice value and taxable value;
- tax treatment, including whether IGST was paid or the supply was made under LUT; and
- the linked shipping bill, bill of export or other customs reference when available.
Include credit notes, debit notes, cancellations and amendments in a separate status column. They should not silently disappear from the population merely because they are not expected to form part of the final claim.
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Download the filed GSTR-1 data
For goods exports, GSTR-1 Table 6A is the relevant export-invoice section identified in the GST Portal instructions. Download the filed data, including any amendments, rather than relying only on the screen view. Where e-invoice details have been auto-populated, use the available download and review it against the invoice register. Auto-population is a starting dataset, not proof that every number, date or tax-treatment selection is correct.
Obtain the customs evidence
Collect the shipping bill or bill of export and the associated export-manifest or export-report status. The GSTR-1 creation instructions identify the customs fields used for an export invoice: port code, shipping bill or bill-of-export number, and its date. Keep the customs document itself so that a reviewer can see whether the number was typed correctly and whether the document belongs to the same invoice.
Confirm return and filing status
Retain proof that the relevant GSTR-3B was validly furnished. Rule 96 links the deemed filing of a goods-export IGST refund to a valid GSTR-3B as well as the export-manifest or export-report condition. The available guidance does not establish a universal, line-by-line GSTR-3B table crosswalk for every exporter, so do not invent a table mapping or a tolerance. Reconcile the return status required for your claim using the current portal and professional review procedures.
Run the goods-export reconciliation step by step
- Freeze the population. Take the sales-register list for the tax period and mark each row as included, excluded with a reason, cancelled, amended or pending customs data. Count the rows and preserve the extraction date so later changes can be explained.
- Match invoice identity to GSTR-1 Table 6A. Search by invoice number and confirm the invoice date. Check that each invoice appears once, that no unrelated invoice has been included, and that an amendment has not created an unintended duplicate. If your system uses leading zeroes, slashes or prefixes differently from the portal, document the normalized comparison and verify the original value before accepting the match.
- Compare monetary values. Compare total invoice value and taxable value with the filed Table 6A values. Investigate rounding, currency conversion, credit notes and any later amendment. Do not assume that a small difference is acceptable; the applicable correction depends on the nature of the difference and the current filing rules.
- Verify the tax-payment selection. Confirm that the GSTR-1 entry indicates the same treatment used for the claim: IGST paid for an IGST-refund route or the appropriate export-without-payment treatment for an LUT/ITC route. A correct invoice with the wrong payment selection can send the transaction into the wrong refund workflow.
- Link the customs record. Enter the port code, shipping bill or bill-of-export number, and date from the customs document. Check that the document describes the same exporter, invoice and goods. A shipping-bill number copied from another invoice is an identity error even if the number itself is valid.
- Check the export-manifest or export-report condition. For a Rule 96 goods-export IGST refund, confirm that the customs export reporting condition has been met. Keep the status evidence with the working paper and flag records that are still pending instead of treating them as ready.
- Check GSTR-3B status. Confirm that the relevant GSTR-3B has been validly furnished. Record the return period and filing date in the reconciliation file. This is a status gate; it is not a substitute for proving the invoice-level values.
- Resolve every mismatch before sign-off. Assign an owner, correction action and completion date to each exception. Do not submit a claim on the assumption that the portal will ignore a discrepancy between customs and GSTR-1.
- Lock the evidence set. Save the final filed GSTR-1 download, amendment details, invoice register, customs documents, export-status evidence and GSTR-3B proof together. Use read-only or version-controlled storage after approval so the claim can be reconstructed later.
How Rule 96 changes the filing date when data differs
Rule 96 of the CGST Rules addresses the refund of IGST paid on goods exported out of India. Rule 96(1)(b) states:
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“Provided that if there is any mismatch between the data furnished by the exporter of goods in Shipping Bill and those furnished in statement of outward supplies in FORM GSTR-1, as amended in FORM GSTR-1A if any, such application for refund of integrated tax paid on the goods exported out of India shall be deemed to have been filed on such date when such mismatch in respect of the said shipping bill is rectified by the exporter;”
Practically, the sentence means that the relevant shipping bill does not reach its deemed application date while the mismatch remains unresolved. The date is tied to rectification by the exporter, not to the date on which the original invoice was issued or the first GSTR-1 was filed. This rule concerns the IGST-paid goods route; it does not turn every export refund into a shipping-bill procedure.
Rule 96 also requires the conditions concerning a valid GSTR-3B and the export-manifest or export-report process. Keep those conditions in the same approval checklist instead of checking only the invoice and shipping-bill numbers.
What to do when shipping-bill details were unavailable
GST Portal guidance permits export invoice details to be filed in GSTR-1 when the shipping bill number and date are not readily available. When the customs details arrive after the original return was filed, the guidance says to report them in the amendment section of GSTR-1 for the month in which they are received.
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- Keep the original export-invoice entry and note that the customs fields were unavailable at filing.
- When the shipping bill or bill of export arrives, verify the number, date and port against the customs document.
- Use the GSTR-1 amendment section for the month in which the details are received, following the portal’s current field labels.
- Download the amended data and re-run the identity and value comparison.
- Check whether any mismatch remains between the amended GSTR-1 data and the shipping bill. The amendment process does not waive the Rule 96 mismatch consequence.
Do not overwrite the original working paper. Retaining both versions shows what was filed initially, when the customs data became available and how the correction was made.
Diagnose common exceptions by field
| Exception | Why it matters | Investigation and correction record |
|---|---|---|
| Invoice missing from Table 6A | The export invoice is not represented in the outward-supplies statement used for the goods-export comparison. | Check whether it was filed in another period, omitted, cancelled or placed in the wrong section. Record the permitted amendment or corrective filing used. |
| Duplicate invoice in Table 6A | One invoice may be counted twice or linked to two customs records. | Compare original and amended entries, identify the valid one and document the treatment of the duplicate. |
| Invoice number or date differs | Customs and GST systems may not identify the same export transaction. | Compare the source invoice, filed GSTR-1 value and shipping bill character by character, including prefixes and date format. Correct the filed data through the applicable mechanism. |
| Shipping-bill number or date differs | Rule 96 treats a shipping-bill/GSTR-1 mismatch as delaying the deemed application date for that shipping bill. | Use the customs document as the source, correct the relevant GSTR-1 data and retain evidence that the mismatch was rectified. |
| Port code is wrong | The customs linkage can fail even when the invoice number is right. | Verify the code against the shipping bill and the portal’s current master data, then document the correction. |
| Total or taxable value differs | The amount reported for the refund route may not agree with the underlying invoice. | Trace the difference to currency conversion, rounding, credit/debit notes or a data-entry error. Do not apply an assumed tolerance. |
| IGST-paid selection does not match the intended route | The transaction can be presented as the wrong kind of refund claim. | Confirm the export invoice, tax payment and LUT treatment, then correct the filing before preparing the claim. |
| e-invoice auto-population differs from the ledger | Auto-populated data may carry an upstream error or an outdated amendment. | Compare the downloaded e-invoice/Table 6A data with the issued invoice and customs record; treat the download as a review source, not final proof. |
Documents to have ready for the claim file
For a goods-export reconciliation, assemble:
- the export sales register and final invoice-level reconciliation;
- filed GSTR-1 data for the original return and every relevant amendment, including Table 6A entries;
- shipping bills or bills of export, with port code, number and date visible;
- evidence of the applicable export-manifest or export-report status;
- proof that the relevant GSTR-3B was validly furnished;
- evidence of IGST payment when using the IGST-refund route, or the LUT and credit records when using the export-without-payment route; and
- the correction log for every exception closed before filing.
Rule 89 identifies a statement containing shipping-bill or bill-of-export numbers and the relevant export-invoice numbers and dates as evidence for an export-of-goods refund application. Treat that statement as part of the application evidence, not as a replacement for the underlying documents.
The portal fields provide a practical minimum checklist—invoice number and date, port code, shipping-bill or bill-of-export number and date, total invoice value, taxable value and whether GST was paid. They are not, by themselves, a complete attachment list for every refund category.
Goods and services require different evidence paths
Goods exported with IGST payment
Use the Rule 96 workflow: reconcile GSTR-1 Table 6A to the shipping bill or bill of export, verify the export-manifest or report condition and confirm a valid GSTR-3B. A mismatch affects when the application is deemed filed for the affected shipping bill.
Goods exported without IGST payment
The broad route is export under LUT and a refund of eligible unutilized ITC. GST Portal guidance identifies Form GST RFD-11 as the LUT form. The claim still needs accurate export-invoice reporting and route-specific evidence, but it should not be described as a refund of IGST paid.
Services exported with IGST payment
Rule 96 refers applications for refund of IGST paid on export of services to RFD-01 under Rule 89. Service exports do not have a goods shipping-bill matching exercise in the same form. Establish the service-export eligibility and the Rule 89 evidence requirements separately.
Services exported without IGST payment
Use the LUT and the applicable Rule 89/RFD-01 process for refund of eligible unutilized ITC. Do not copy the goods checklist without adapting it to service-export documents and eligibility conditions.
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- Every export invoice in the population has one documented disposition.
- Invoice number and date agree between the source invoice, GSTR-1 and the customs record where applicable.
- Total invoice value and taxable value have been compared and exceptions explained.
- Table 6A payment selection agrees with the chosen refund route.
- Port code and shipping-bill or bill-of-export number and date are copied from the customs document.
- Late-arriving customs details were amended in the GSTR-1 month in which they were received.
- No shipping-bill/GSTR-1 mismatch remains unresolved for an IGST-paid goods claim.
- The export-manifest or export-report condition has been checked.
- The relevant GSTR-3B was validly furnished.
- The Rule 89 statement and route-specific evidence are complete for the claim being filed.
- A second reviewer has signed or otherwise approved the final exception log.
Illustrative exception timeline
Suppose an exporter files an export invoice in GSTR-1 before the shipping bill number and date are available. The invoice remains in the original population, but the customs fields are marked pending. When the shipping bill arrives, the exporter verifies the port, number, date and values, reports the details in the amendment section for the month received, downloads the amended GSTR-1 data and checks the shipping-bill match again. If the amended data still differs from the shipping bill, the Rule 96 deemed filing date has not been reached for that shipping bill until the exporter rectifies the mismatch. This example illustrates the control sequence; the actual correction fields and eligibility depend on the transaction and the current portal.
Limits of a generic reconciliation template
There is no single published GSTR-3B table crosswalk, universal portal mismatch-code catalogue or one attachment list that applies to every export refund route. The required values and documents depend on goods versus services, IGST payment versus LUT, amendments and the current GST Portal workflow. If a claim includes unusual amendments, multiple shipping bills, credit notes or a service-export eligibility issue, obtain transaction-specific tax advice rather than filling gaps with assumed tolerances.
Final filing gate
File only after the invoice register, GSTR-1 (including amendments), customs record, export-status evidence and GSTR-3B status tell the same story for every included transaction. For an IGST-paid goods export, an unresolved shipping-bill/GSTR-1 mismatch is not a minor formatting issue: Rule 96 postpones the deemed application date until the exporter rectifies it. Selecting the route first and preserving a complete, invoice-level evidence trail is the most reliable way to prevent a refund claim from being delayed by avoidable data differences.
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